Genome-wide profiling of novel and conserved <Emphasis Type="Italic">Populus</Emphasis> microRNAs involved in pathogen stress response by deep sequencing |
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Authors: | Lei Chen Yuanyuan Ren Yiyun Zhang Jichen Xu Zhiyi Zhang Yanwei Wang |
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Institution: | (1) National Engineering Laboratory for Tree Breeding, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Biotechnology, Beijing Forestry University, 100083 Beijing, People’s Republic of China; |
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Abstract: | MicroRNAs (miRNAs) are small RNAs, generally of 20–23 nt, that down-regulate target gene expression during development, differentiation,
growth, and metabolism. In Populus, extensive studies of miRNAs involved in cold, heat, dehydration, salinity, and mechanical stresses have been performed;
however, there are few reports profiling the miRNA expression patterns during pathogen stress. We obtained almost 38 million
raw reads through Solexa sequencing of two libraries from Populus inoculated and uninoculated with canker disease pathogen. Sequence analyses identified 74 conserved miRNA sequences belonging
to 37 miRNA families from 154 loci in the Populus genome and 27 novel miRNA sequences from 35 loci, including their complementary miRNA* strands. Intriguingly, the miRNA*
of three conserved miRNAs were more abundant than their corresponding miRNAs. The overall expression levels of conserved miRNAs
increased when subjected to pathogen stress, and expression levels of 33 miRNA sequences markedly changed. The expression
trends determined by sequencing and by qRT-PCR were similar. Finally, nine target genes for three conserved miRNAs and 63
target genes for novel miRNAs were predicted using computational analysis, and their functions were annotated. Deep sequencing
provides an opportunity to identify pathogen-regulated miRNAs in trees, which will help in understanding the regulatory mechanisms
of plant defense responses during pathogen infection. |
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